move spot data to processed data document

Author: oscar-castro-bl

src/allotropy/allotrope/schema_mappers/adm/plate_reader/benchling/_2023/_09/plate_reader.py

@@ -86,7 +86,6 @@ class ImageFeature:
     feature: str
     result: float | InvalidJsonFloat
     data_sources: list[DataSource] | None = None
-    custom_info: dict[str, Any] | None = None
 
 
 @dataclass(frozen=True)
@@ -562,18 +561,15 @@ def _get_processed_data_aggregate_document(
                     processed_data_identifier=data.identifier,
                     image_feature_aggregate_document=ImageFeatureAggregateDocument(
                         image_feature_document=[
-                            add_custom_information_document(
-                                ImageFeatureDocumentItem(
-                                    image_feature_identifier=image_feature.identifier,
-                                    image_feature_name=image_feature.feature,
-                                    image_feature_result=TQuantityValueUnitless(
-                                        value=image_feature.result
-                                    ),
-                                    data_source_aggregate_document=self._get_data_source_aggregate_document(
-                                        image_feature.data_sources
-                                    ),
+                            ImageFeatureDocumentItem(
+                                image_feature_identifier=image_feature.identifier,
+                                image_feature_name=image_feature.feature,
+                                image_feature_result=TQuantityValueUnitless(
+                                    value=image_feature.result
+                                ),
+                                data_source_aggregate_document=self._get_data_source_aggregate_document(
+                                    image_feature.data_sources
                                 ),
-                                image_feature.custom_info,
                             )
                             for image_feature in data.features
                         ]

src/allotropy/parsers/ctl_immunospot/ctl_immunospot_structure.py

@@ -36,11 +36,6 @@ def _create_measurement(
     header_data: dict[str, float | str | None],
 ) -> Measurement:
     location_identifier = f"{well_row}{well_col}"
-    image_custom_info = {
-        "Min. SpotSize": header_data.pop("Min. SpotSize", None),
-        "Max. SpotSize": header_data.pop("Max. SpotSize", None),
-        "Spot Separation": header_data.pop("Spot Separation", None),
-    }
     return Measurement(
         type_=MeasurementType.OPTICAL_IMAGING,
         device_type=constants.DEVICE_TYPE,
@@ -51,12 +46,16 @@ def _create_measurement(
         detection_type=constants.DETECTION_TYPE,
         processed_data=ProcessedData(
             identifier=random_uuid_str(),
+            data_processing_document={
+                "Min. SpotSize": header_data.pop("Min. SpotSize", None),
+                "Max. SpotSize": header_data.pop("Max. SpotSize", None),
+                "Spot Separation": header_data.pop("Spot Separation", None),
+            },
             features=[
                 ImageFeature(
                     identifier=random_uuid_str(),
                     feature=name,
                     result=float(data[well_col][well_row]),
-                    custom_info=image_custom_info,
                 )
                 for name, data in plate_data.items()
             ],
@@ -115,7 +114,12 @@ def create_measurement_groups(
             analyst=analyst,
             measurements=[
                 _create_measurement(
-                    row, col, well_plate_identifier, plate_data, histograms, header_data
+                    row,
+                    col,
+                    well_plate_identifier,
+                    plate_data,
+                    histograms,
+                    header_data.copy(),
                 )
             ],
             custom_info=custom_info,